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Gold nanoparticles for high-throughput genotyping of long-range haplotypes

Nature Nanotechnology volume 6, pages 639–644 (2011)Cite this article

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Abstract

Completion of the Human Genome Project1 and the HapMap Project2 has led to increasing demands for mapping complex traits in humans to understand the aetiology of diseases3. Identifying variations in the DNA sequence, which affect how we develop disease and respond to pathogens and drugs, is important for this purpose, but it is difficult to identify these variations in large sample sets3,4,5. Here we show that through a combination of capillary sequencing and polymerase chain reaction assisted by gold nanoparticles, it is possible to identify several DNA variations that are associated with age-related macular degeneration6,7,8 and psoriasis9 on significant regions of human genomic DNA. Our method is accurate and promising for large-scale and high-throughput genetic analysis of susceptibility towards disease and drug resistance10,11,12.

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Figure 1: Schematic showing the AuNPs-enhanced allele-specific sequencing (AuNAS) strategy.
Figure 2: Real-time amplification curves and Ct values of AS-PCR and AuNPs-enhanced AS-PCR using 5 nm AuNPs.
Figure 3: Chromosome separation using AuNPs-enhanced AS-PCR.
Figure 4: Reconstruction of the whole haplotype for wet AMD using AuNPs-enhanced allele-specific sequencing.

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References

  1. McPherson, J. D. et al. A physical map of the human genome. Nature 409, 934–941 (2001).

    Article  CAS  Google Scholar 

  2. Frazer, K. A. & Consortium, T. I. H. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).

    Article  CAS  Google Scholar 

  3. Douglas, J. A., Boehnke, M., Gillanders, E., Trent, J. M. & Gruber, S. B. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nature Genet. 28, 361–364 (2001).

    Article  CAS  Google Scholar 

  4. Xiao, M. et al. Direct determination of haplotypes from single DNA molecules. Nature Methods 6, 199–201 (2009).

    Article  CAS  Google Scholar 

  5. Kwok, P. Y. & Xiao, M. Single-molecule analysis for molecular haplotyping. Hum. Mutat. 23, 442–446 (2004).

    Article  CAS  Google Scholar 

  6. DeWan, A. et al. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314, 989–992 (2006).

    Article  CAS  Google Scholar 

  7. Fritsche, L. G. et al. Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA. Nature Genet. 40, 892–896 (2008).

    Article  CAS  Google Scholar 

  8. Kanda, A. et al. A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Proc. Natl Acad. Sci. USA 104, 16227–16232 (2007).

    Article  CAS  Google Scholar 

  9. Zhang, X. J. et al. Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. Nature Genet. 41, 205–210 (2009).

    Article  CAS  Google Scholar 

  10. Collins, F. S., Guyer, M. S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580–1581 (1997).

    Article  CAS  Google Scholar 

  11. Folstein, S. & Rutter, M. Genetic influences and infantile autism. Nature 265, 726–728 (1977).

    Article  CAS  Google Scholar 

  12. Collins, F. S., Brooks, L. D. & Chakravarti, A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229–1231 (1998).

    Article  CAS  Google Scholar 

  13. Kwok, P. Y. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genom. Hum. Genet. 2, 235–258 (2001).

    Article  CAS  Google Scholar 

  14. Beaudet, A. L. & Belmont, J. W. Array-based DNA diagnostics: let the revolution begin. Ann. Rev. Med. 59, 113–129 (2008).

    Article  CAS  Google Scholar 

  15. Rosi, N. L. & Mirkin, C. A. Nanostructures in biodiagnostics. Chem. Rev. 105, 1547–1562 (2005).

    Article  CAS  Google Scholar 

  16. Lu, Y. & Liu, J. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical stimuli. Acc. Chem. Res. 40, 315–323 (2007).

    Article  CAS  Google Scholar 

  17. Li, H. et al. Nanoparticle PCR: nanogold-assisted PCR with enhanced specificity. Angew. Chem. Int. Ed. 44, 5100–5103 (2005).

    Article  CAS  Google Scholar 

  18. Li, M., Lin, Y. C., Wu, C. C. & Liu, H. S. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic Acids Res. 33, e184 (2005).

    Article  Google Scholar 

  19. Mi, L. et al. Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. Small 5, 2597–2600 (2009).

    Article  CAS  Google Scholar 

  20. Rosi, N. L. et al. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical stimuli. Science 312, 1027–1030 (2006).

    Article  CAS  Google Scholar 

  21. Li, H. & Rothberg, L. Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc. Natl Acad. Sci. USA 101, 14036–14039 (2004).

    Article  CAS  Google Scholar 

  22. Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    Article  CAS  Google Scholar 

  23. Herdt, A. R., Drawz, S. M., Kang, Y. & Taton, T. A. DNA dissociation and degradation at gold nanoparticle surfaces. Colloid. Surface. B 51, 130–139 (2006).

    Article  CAS  Google Scholar 

  24. Tost, J. et al. Molecular haplotyping at high throughput. Nucleic Acids Res. 30, e96 (2002).

    Article  Google Scholar 

  25. Voelkerding, K. V., Dames, S. & Durtschi, J. D. Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy. J. Mol. Diag. 12, 539–551 (2010).

    Article  Google Scholar 

  26. Shendure, J. & Ji, H. Next-generation DNA sequencing. Nature Biotechnol. 26, 1146–1153 (2008).

    Article  Google Scholar 

  27. Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989 (2001).

    Article  CAS  Google Scholar 

  28. Levenstien, M. A., Ott, J. & Gordon, D. Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes. PLOS Genet. 2, e127 (2006).

    Article  Google Scholar 

  29. Fan, H. C., Wang, J., Potanina, A. & Quake, S. R. Whole-genome molecular haplotyping of single cells. Nature Biotechnol. 29, 51–57 (2010).

    Article  CAS  Google Scholar 

  30. Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnol. 29, 59–63 (2010).

    Article  Google Scholar 

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Acknowledgements

This work was supported by the National 863 Program (2009AA022701), the National 973 Program (2010CB529602, 2007CB936000, 2012CB932600), the Natural Science Foundation of China (20725516, 31000553, 90913014, 20902096), the Foundation for the Author of National Excellent Doctoral Dissertation of PR China (201026), the Program for New Century Excellent Talents in University (NCET-09-0550), the Shanghai Changning Health Bureau Program (2008406002), the Shanghai Municipal Health Bureau Program (2008095), the Shanghai Leading Academic Discipline Project (B205), CAS (KJCX2-EW-N03) and the Major S&T Program (2009ZX10004-301).

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  1. Peng Chen and Dun Pan: These authors contributed equally to this work

Authors and Affiliations

  1. Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China

    Peng Chen, Chunhai Fan, Jianhua Chen, Ke Huang, You Li, Guoyin Feng, Lin He & Yongyong Shi

  2. Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China

    Dun Pan, Chunhai Fan, Dongfang Wang & Honglu Zhang

  3. School of Life Science and Technology, Shanghai Jiao Tong University, Shanghai, 200030, China

    Peiji Liang

  4. Institute for Nutritional Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Lin He

  5. Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China

    Lin He

  6. Changning Mental Health Center, Shanghai, 200042, China

    Yongyong Shi

Authors
  1. Peng Chen
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  9. Guoyin Feng
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Contributions

Y.S. and C.F. conceived and designed the experiments. P.C., D.P., J.C., D.W. and H.Z. performed the experiments. J.C. and P.C. analysed the data. K.H., Y.L., P.L. and L.H. contributed materials/analysis tools. Y.S. and G.F. collected DNA samples. P.C., D.P., C.F. and Y.S. co-wrote the paper. P.C. and D.P. contributed equally to this work. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Chunhai Fan or Yongyong Shi.

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The authors declare no competing financial interests.

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Chen, P., Pan, D., Fan, C. et al. Gold nanoparticles for high-throughput genotyping of long-range haplotypes. Nature Nanotech 6, 639–644 (2011). https://doi.org/10.1038/nnano.2011.141

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